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Research Areas

Multiscale & coarse-grained modelling, biomolecular simulation, lipid membrane dynamics, infectious disease, host-pathogen interactions, structural virology, microbial pathogenesis, therapeutics design.

Research Interests

We develop computational models that integrate diverse biophysical and biochemical data to resolve the dynamics of biomolecules over multiple time and length scales, focusing particularly on mechanisms of infectious disease, the host immune response to pathogens, and ultimately, therapeutic intervention strategies. Recent research highlights in the structural virology field include the development of a “virtual dengue virus” as part of an MOE Tier 3 consortium, which is now being extended towards new rational approaches for vaccine and antibody design, funded by an NRF CRP grant. Recent progress has also been made in the area of bacterial pathogenesis, via the discovery of previously undisclosed natural defense and antiseptic mechanisms in wound healing, which may be leveraged to develop new ways to fight infections and inflammatory diseases.

Selected Publications

1. Huber RG, Lim XN, Ng WC, Sim AYL, Poh HX, Shen Y, Lim SY, Sundstrom KB, Sun X, Aw JG, Too HK, Boey PH, Wilm A, Chawla T, Choy MM, Jiang L, de Sessions PF, Loh XJ, Alonso S, Hibberd M, Nagarajan N, Ooi EE, Bond PJ, Sessions OM, Wan Y. (2019). Structure mapping of dengue and Zika viruses reveals functional long-range interactions. Nature Commun. 10:1408.

2. Chan KW, Watanabe S, Jin JY, Pompon J, Teng D, Alonso S, Vijaykrishna D, Halstead SB, Marzinek JK, Bond PJ, Burla B, Torta F, Wenk MR, Ooi EE, Vasudevan SG. (2019). Dengue disease severity caused by elevated levels of secreted NS1 arising from a single T164S substitution. Science. Transl. Med. In press.

3. Cai S, Lukamto DH, Toh JKC, Huber RG, Bond PJ, Jee JE, Lim TC, Liu P, Chen L, Qu QV, Lee SS, Lee SG. (2019). Directing GDNF-Mediated Neuronal Signaling with Proactively Programmable Cell-Surface Saccharide-Free Glycosaminoglycan Mimetics. ChemComm. 55:1259-62.

4. Wirawan M, Fibriansah G, Marzinek JK, Lim XX, Ng TS, Sim AYL, Zhang Q, Kostyuchenko VA, Shi J, Smith SA, Verma CS, Anand G, Crowe Jr. JE, Bond PJ, Lok SM. (2019). Mechanism of enhanced immature dengue virus attachment to endosomal membrane induced by prM antibody. Structure. 27:253-67.

5. Lim TC, Cai S, Huber RG, Bond PJ, Chia PXS, Khou SL, Gao S, Lee SS, Lee SG. (2018). Facile Saccharide-free Mimetics that Recapitulate Key Features of Glycosaminoglycan Sulfation Patterns. Chem. Sci. 9:7940-7.

6. Sharma KK, Lim XX, Tantirimudalige SN, Gupta A, Marzinek JK, Holdbrook D, Lim XYE, Bond PJ, Anand G, Wohland T. (2019). Infectivity of dengue virus serotypes 1 and 2 is correlated to E protein intrinsic dynamics but not to envelope conformations. Structure. 27:618-30.e4.

7. Saravanan R, Holdbrook DA, Petrlova J, Singh S, Berglund NA, Choong YK, Bond PJ, Malmsten M, Schmidtchen A. (2018). Structural basis for endotoxin neutralization and anti-inflammatory activity of thrombin-derived C-terminal peptides. Nature Commun. 9:2762.

8. Huber RG, Berglund NA, Kargas V, Marzinek JK, Holdbrook DA, Khalid S, Piggot TJ, Schmidtchen A, Bond PJ. (2018). A thermodynamic funnel drives bacterial lipopolysaccharide transfer in the TLR4 Pathway. Structure. 26:1151-61.

9. Yeow J, Tan KW, Holdbrook DA, Chong ZS, Marzinek JK, Bond PJ, Chng SS. (2018). The architecture of the OmpC–MlaA complex sheds light on the maintenance of outer membrane lipid asymmetry in Escherichia coli. J. Biol. Chem. 20:11325-40.

10. Boon PLS, Saw WG, Lim XX, Raghuvamsi PV, Huber RG, Marzinek JK, Holdbrook DA, Anand GS, Grüber G, Bond PJ. (2018). Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble. ACS Chem. Biol. 13:1621-30.

11. Marzinek JK, Bag N, Huber RG, Holdbrook DA, Wohland T, Verma CS, Bond PJ. (2018). A Funneled Conformational Landscape Governs Flavivirus Fusion Peptide Interaction with Lipid Membranes. J. Chem. Theory Comput. 14:3920-32.

12. Lancaster GI, Langley KG, Berglund NA, Kammoun HL, Reibe S, Estevez E, Weir J, Mellett NA, Pernes G, Conway JRW, Lee MK, Timpson P, Murphy AJ, Masters SL, Gerondakis S, Baronicek N, Kaczorowski DC, Dinger ME, Meikle PJ, Bond PJ, Febbraio MA. (2018). Evidence that TLR4 is not a receptor for saturated fatty acids but mediates lipid-induced inflammation by re-programming macrophage metabolism. Cell Metab. 27:1096-110.e5.

13. Chambers JE, Kubánková M, Huber RG, López-Duarte I, Avezov E, Bond PJ, Marciniak SJ, Kuimova MK. (2018). An optical technique for mapping microviscosity dynamics in cellular organelles. ACS Nano. 12:4398-407

14. Latty S, Sakai J, Hopkins L, Verstak B, Paramo T, Berglund NA, Cammorota E, Cicuta P, Gay NJ, Bond PJ, Klenerman D, Bryant CE. Activation of Toll-like receptors nucleates assembly of the MyDDosome signaling hub. (2018). Elife. 7:e31377.

15. Petrlovaa J, Hansen FC, van der Plas MJA, Huber RG, Mörgelin M, Malmsten M, Bond PJ, Schmidtchen A. (2017). Aggregation of thrombin-derived C-terminal fragments – a novel host defense mechanism. Proc. Natl. Acad. Sci. USA. 114:E4213-22.

16. Holdbrook DA, Burmann BM, Huber RG, Petoukhov MV, Svergun DI, Hiller S, Bond PJ. (2017). A Spring-Loaded Mechanism Governs the Clamp-Like Dynamics of the Skp Chaperone. Structure. 25:1079-88.

17. Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S. (2017). Progress in Molecular Dynamics Simulations of Bacterial Cell Envelopes. J. Phys. Chem. Lett. 8:2513-8.

18. Fukuda Y, Cheong PL, Lynch J, Brighton C, Frase S, Kargas V, Rampersaud E, Wang Y, Sankaran VG, Yu B, Ney PA, Weiss M, Vogel P, Bond PJ, Trent RJ, Ford RC, Schuetz JD. (2016). The severity of hereditary porphyria is modulated by the porphyrin exporter and Lan antigen ABCB6. Nature Commun. 7:12353.

19. Santos-Moreno J, East A, Guilvout I, Nadeau N, Bond PJ, Nhieu GTV, Francetic O. (2017). Polar N-terminal residues conserved in type 2 secretion pseudopilins determine subunit targeting and membrane extraction steps during fibre assembly. J. Mol. Biol. 429:1746-65.

20. Marzinek JK, Holdbrook D, Huber RG, Verma C, Bond PJ. (2016). Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations. Structure. 24:1410-20.